tbuckley/cabot-search huggingface dataset:
TMIC-49. CHITINASE-3-LIKE 1 PROTEIN COMPLEXES REGULATE PD-1 SIGNALING-MEDIATED IMMUNOSUPPRESSION IN GLIOBLASTOMA
Authors: Rashmi Srivastava, Apeng Chen, Meghana Dodda, Han Zou, Baoli Hu
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma (GBM), the most common and lethal brain tumor with a median survival rate of only 15 months, remains largely incurable despite intensive multimodal treatment, including immunotherapeutic strategies being tested in clinical trials. GBM is highly immunosuppressive and resistant to immunotherapy because glioma cells escape from effective antitumor immunity through programing the tumor microenvironment (TME). Owing to the tremendous heterogeneity and plasticity of tumor cells and the surrounding TME, understanding the mechanisms of immune evasion by GBM remains elusive. We have recently discovered that the Chitinase-3-like-1 (CHI3L1)-Galectin-3 (Gal3) protein binding complex can selectively promote tumor-associated macrophage migration and infiltration with a protumor M2-like phenotype and T cell-mediated immunosuppression, which are governed by a transcriptional program of NF-κB/CEBPβ in the CHI3L1/Gal3-PI3K/AKT/mTOR axis. The immunoprecipitation coupled to liquid chromatography-mass spectrometry analysis revealed that galectin 3–binding protein (Gal3BP) competes with Gal3 to bind with CHI3L1 for negative regulation of the CHI3L1-Gal3 mediated processes. Interestingly, a newly-developed Gal3BP mimetic peptide can disrupt CHI3L1-Gal3 interaction, resulting in decreasing migration of M2-like bone marrow-derived macrophages (BMDMs), increasing CD8+ T cell infiltration, reversing immunosuppression, and inhibiting tumor progression in vitro and in vivo. Analyzing PD-1 signaling activation, we found that the Gal3BP mimetic peptide significantly decreased PD-L1 expression in tumor cells. Correlation analysis showed that CHI31L and Gal3 (encoded by LGALS3 gene) are significantly associated with both PD-L1 and PD-L2 in GBM patient samples. Furthermore, overexpression of CHI3L1 increased expression levels of PD-L1 and PD-L2, and CHI3L1 deletion decreased their expression in GBM patient-derived neurosphere lines. The treatment with recombinant CHI3L1 protein significantly increased PD-L1 and PD-L2 expression in M2-like BMDMs (with high levels of endogenous Gal3). Collectively, these data suggest that CHI3L1 protein complexes control the GBM immunosuppressive microenvironment by PD-1/PD-L1/PD-L2 signaling, providing new immunotherapeutic strategies for this brain cancer.
TMIC-48. HYPOXIC AND PERI-NECROTIC ZONES IN GLIOBLASTOMA CAUSE HIPPO-OFF SIGNALING, POTENTIALLY SUPPORTING GLIOMA STEM CELLS
Authors: Ling-Kai Shih, Jiabo Li, Steven Markwell, Tatiana Carneiro-Lobo, Cheryl Olson, Daniel Brat
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma (GBM) is the most common and malignant primary brain tumor with pre-necrotic and post-necrotic growth phases. The development of necrosis is associated with extensive tumor micro-environmental (TME) rearrangement and rapid biologic advancement. Compared to pre-necrotic GBMs, post-necrotic GBMs are heterogenous and contain multi-focal regions of necrosis surrounded by pseudopalisading cells and characterized by severe hypoxia. Hypoxic, peri-necrotic zones are highly enriched for glioma stem cells (GSCs) and tumor associated macrophages (TAMs), the latter accounting for 30-40% total tumor cellularity. Using Ivy-GAP data, we performed gene set enrichment analysis (GSEA) for stem-cell associated markers, comparing peri-necrotic to non-necrotic regions. We also used TCGA/CGGA data to identify correlations between hypoxia markers and classic stem-cell associated markers (SOX2, SOX9, nestin, STAT3, prominin). None of these showed enrichment in the peri-necrotic zone or association with hypoxia markers. However, we uncovered strong associations of Hippo-off signaling with peri-necrotic regions, signifying activation of YAP/TAZ transcriptional activation. We therefore hypothesized that Hippo-off (YAP/TAZ transcriptional activation) in hypoxic peri-necrotic zones promotes GSC self-renewing division. To support this, we performed GSEA for Hippo pathway readout genes and found peri-necrotic enrichment of Hippo regulated genes CYR61, BIRC2, SERPINE1 and AREG. Using patient-derived GBM neurosphere cultures, we exposed glioma cells to 1% hypoxia and found that p-YAP1 and p-TAZ protein levels were downregulated compared to normoxia (21%) at 24 hrs, correlating with Hippo-on. Hippo pathway gene targets were also upregulated, indicating activation of YAP/TAZ transcription. Using Ivy-GAP, TCGA and CGGA data, we also found peri-necrotic/hypoxic enrichment of two cytokines, IL-1β and IL-6, known to trigger YAP/TAZ activation. Using cytokine multiplex analysis, we observed an upregulation in both IL-1β and IL-6 secretion from hypoxic monocytes and microglia, raising the possibility that these cytokines directly stimulate Hippo-off and promote GSC self-renewing division in the GBM peri-necrotic niche.
TMIC-73. HIGH-DIMENSIONAL HISTOPATHOLOGIC EVALUATION OF THE HYPOXIC MICROENVIRONMENT IN GLIOBLASTOMA
Authors: Sheila Mansouri, Mark Zaidi, Olivia Singh, Hafsah Ali, Shirin Karimi, Phoebe Lombard, Anna Dvorkin-Gheva, Carlos Velasquez, Kaviya Devaraja, Julio Sosa, Vikas Patil, Qingxia Wei, Ronald Wu, Mira Li, May Cheung, Mathew Voisin, Andrew Gao, David Hedley, Kenneth Aldape, Bradly Wouters, Gelareh Zadeh
Journal: Neuro-Oncology (2022)

Abstract Rapidly growing solid tumors such as glioblastoma (GBM) are characteristically hypoxic, displaying large areas of necrosis surrounded by hyperproliferative pseudopalisading cells. Intra-tumoral hypoxia develops over time in the three-dimensional space and the degree of tissue oxygenation is a dynamic process that varies continuously. Combined with the extensive inter- and intra-tumoral heterogeneity associated with GBM at the bulk and single cell level, hypoxia contributes to a gradient of molecular alterations that are specific to the different cell populations that make up the bulk of the tumor and reside in specific niches. To date, high dimensional histopathologic analyses of the hypoxic regions within GBM tissue have not been performed. Here, we took a combined spatial and single-cell proteomic profiling approach to investigate the histopathologic features of hypoxia by leveraging a unique clinical study where the exogenous hypoxia marker pimonidazole (PIMO) is administered to patients with GBM prior to surgery. Tissue specimens were subjected to imaging mass cytometry and serial immunohistochemistry using a panel of 27 markers associated with cellular hallmarks of hypoxia, metabolism, proliferation, stemness, angiogenesis, and immune cell types. We took high-resolution imaging and statistical approaches to explore the interplay of the different markers within hypoxic regions of primary and recurrent GBMs, in addition to IDH-mutant gliomas. Our findings elucidate the expression pattern of key biological markers relative to one another, altered composition of different cell types, along with differential proliferative, transcriptional, and translational activation states associated with each cell type within the hypoxic regions of GBM.
TMET-29. THE GLUTAMINE TRANSPORTER SLC1A5 IS ASSOCIATED WITH REWIRING OF AMINO ACID, LIPID, AND IMMUNE PATHWAYS AND TUMOR PROGNOSIS IN PEDIATRIC BRAIN CANCERS
Authors: Adam A Kraya, Run Jin, Chao Zhao, Ariana Familiar, Philip B Storm, Kathryn Wellen, Adam C Resnick, Ali Nabavizadeh
Journal: Neuro-Oncology (2022)

Abstract Glutamine transporters play an important role in supporting increased tumor nutritional demands, often through overexpression of the solute carrier (SLC) family of membrane transporters. We aimed to understand the relationship of SLC transporter expression with pediatric brain tumor subtypes, lipid metabolism and their potential prognostic significance using data from the Pediatric Brain Tumor Atlas (PBTA). Using the expression of amino acid transporter genes, we found that elevated expression of glutamine transporters (SLC1A5, SLC7A5, SLC7A11, SLC38A5, SLC38A3) predicted shorter progression-free survival (PFS) in low-grade gliomas (LGGs) and poorer overall survival in pediatric ependymomas, high-grade gliomas (HGGs), and medulloblastomas. We focused specifically on SLC1A5 given the availability of imaging probes (18 F-Fluoroglutamine and 18F-Fluciclovine) for the corresponding amino acid transporter (ASCT2). Kaplan-Meier analysis found that higher expression of SLC1A5 was associated with shorter OS in ependymoma and medulloblastoma (p = 0.032 and p = 9.8e-4) and shorter PFS in LGG (p = 0.022). We found a universally higher expression of ATP citrate lyase (ACLY) and Acetyl-CoA carboxylase 1 (ACC) relative to normal brain tissue across all histologies. BRAF driven low grade gliomas and SHH-driven medulloblastomas showed differential expression of ACLY compared to other histologies. In addition, Acyl-CoA synthetase short chain family member 1 and 2 (ACSS1 and 2) were universally downregulated in pediatric gliomas, indicating that pediatric CNS tumors seem to rely on ACLY over ACSS for lipid synthesis. Gene set analysis showed higher expression and network rewiring of amino acid, lipid, and immune pathways in SLC1A5-high expressing clusters. SLC1A5 correlated negatively with pathways associated with lipid metabolic breakdown/degradation and correlated positively with pathways associated with lipid biosynthesis. In conclusion, our work demonstrates that glutamine transporters, particularly SLC1A5, represent compelling targets in pediatric brain tumors and can be exploited with theranostic approaches and amino-acid PET imaging.
TMET-39. INHIBITION OF THE TCA-CYCLE IS SYNTHETICALLY LETHAL WITH LOSS OF FUNCTION OF BCL-XL IN GLIOBLASTOMA
Authors: Trang Nguyen, Enyuan Shang, Consuelo Torrini, Chang Shu, Mike-Andrew Westhoff, Georg Karpel-Massler, Markus Siegelin
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma (GBM) remains an incurable disease, requiring more effective therapies. Through CRISPR and RNAi library screening interrogation we identified several TCA-cycle enzymes as essential for GBM growth. By combining a transcriptome and metabolite screening analyses we discovered that inhibition of the TCA-cycle by the clinically validated drug compound, CPI-613, is synthetically lethal with Bcl-xL loss of function (genetically and through the clinically validated BH3-mimetic, ABT263) in patient-derived xenograft as well neurosphere GBM cultures. Carbon tracing experiments (U-13 C-glucose and U-13 C-glutamine) and extracellular flux analysis showed that CPI-613 interferes with mitochondrial respiration. In turn, CPI-613 mediated energy deprivation drives an integrated stress response with an up-regulation of the BH3-only domain protein, Noxa in an ATF4 dependent manner as demonstrated by genetic loss of function experiments. Consistently, silencing of Noxa rescued from cell death induced by CPI-613 as well as by the combination treatment of ABT263 and CPI-613 in model systems of GBM. In patient-derived xenograft models of GBM in mice, the combination treatment of ABT263 and CPI613 suppressed tumor growth more potently than each compound on its own. Therefore, combined inhibition of Bcl-xL along with interference of the TCA-cycle might be a novel treatment strategy for GBM.
TMET-15. CYTOCHROME C OXIDASE MEDIATES CELLULAR IRON HOMEOSTASIS AND RADIORESISTANCE IN GLIOBLASTOMA
Authors: Md Yousuf Ali, Casey Pullium, Susanne Flor, Prabhat Goswami, Claudia Oliva, Corinne Griguer
Journal: Neuro-Oncology (2022)

Abstract Defining the molecular mechanism(s) responsible for the adaptive radioresistance in glioblastoma (GBM) is necessary for the development of effective treatment options. The cellular labile iron pool (LIP) is very important for determining the cellular response to radiation, as it contributes to radiation-induced production of reactive oxygen species (ROS). Recently, cytochrome c oxidase (CcO), a mitochondrial heme-containing enzyme also involved in regulating ROS production, was found to be involved in GBM chemoresistance. However, the role of LIP and CcO in GBM radioresistance is not known. Herein, we tested the hypothesis that CcO-mediated alterations in the level of labile iron contribute to adaptive radioresistance. Using an in vitro model of GBM adaptive radioresistance, we found an increase in CcO activity in radioresistant cells that associated with a decrease in the cellular LIP (4.1-fold), decrease in lipid peroxidation (2-fold), and a switch in the CcO subunit 4 (COX4) isoform expression, from COX4-2 to COX4-1. Furthermore, knockdown of COX4-1 in radioresistant GBM cells decreased CcO activity and restored radiosensitivity, whereas overexpression of COX4-1 in radiosensitive cells increased CcO activity and rendered the cells radioresistant. We further observed that radioresistant cells has increased expression of mitoferrin-1, a protein that facilitates the incorporation of iron into mitochondria. Overexpression of mitoferrin-1 in glioma cells increases the activity of mitochondrial protein complexes, decreases the cellular labile iron pool (p&amp;lt; 0.05), and decreases the production of 4-hydroxy nonenal (4-HNE), a lipid peroxidation product. Furthermore, overexpression of mitoferrin-1 significantly increases the anchorage independent colony formation in soft agar assay (p&amp;lt; 0.01). Moreover, mitoferrin-1 overexpressing cells implanted orthotopically in the brain of nude mice significantly decreased survival compared to wild type (p &amp;lt; 0.01). These results indicate that manipulation of cellular and mitochondrial iron homeostasis may provide a strategy to improve therapeutic outcome in patients with GBM.
NCOG-46. PERSONALIZED, PARCEL-GUIDED RTMS FOR NEURO-REHABILITATION AFTER TUMOR NEUROSURGERY: SAFETY AND PROOF OF CONCEPT
Authors: Jacky Yeung, Jessica Tang, Jonas Holle, Charles Teo, Michael Sughrue
Journal: Neuro-Oncology (2022)

Abstract Deficits in neurological and psychocognitive function are common for patients who have undergone surgical removal of primary tumors. Repetitive Transcranial Magnetic Stimulation (rTMS) is an emerging non-invasive tool used for the treatment of neuropsychiatric disorders. We present a retrospective review of individualized, targeted rTMS in thirteen patients who presented with post-operative neurological deficits following craniotomy for tumor resection. Multiple cortical targets were selected based on the patient’s neurological disorder, the networks associated with the deficit, and anomalies in the functional connectivity of the patient’s brain as determined by machine-learning. TMS treatment was performed for 5 consecutive days. EuroQol quality of life (EQ-5D), functional extremity scales, and neuropsychiatric questionnaires related to the patient’s deficit were assessed prior to rTMS treatment, after treatment, and during follow-up. Five patients (38.5%) had glioblastomas; four patients (30.8%) had oligodendrogliomas; two patients (15.4%) had astrocytoma; one patient (7.7%) had ganglioglioma; and one patient (7.7%) had a pineal cyst. All thirteen patients reported significantly improved quality of life after rTMS treatment (p = 0.0065) and during follow-up (p = 0.0038) as compared to baseline. For patients with functional deficits, lower extremity functional scale (LEFS) was significantly improved one week after rTMS treatment (p = 0.0205). Upper extremity function scale (UEFS) showed non-significant trend in improvement after rTMS treatment (p = 0.0777). In the two patients who developed post-craniotomy depression, they showed a 26% and 88% reduction in depressive symptoms based on the Beck’s Depression Inventory (BDI) at two-month follow-up. These results suggest that the personalized, functional connectivity approach to rTMS target and treatment may be effective for patients with post-craniotomy functional impairments and neuropsychiatric disorders. This method of post-operative interventional neuro-rehabilitation is safe, noninvasive, and allows for the simultaneous treatment of multiple symptoms.
MODL-03. IDH-MUTANT GLIOMA GWAS ALLELE RS55705857 ON 8Q24 IS CHANGING THE DYNAMICS OF UNPATTERNED CEREBRAL ORGANOID DEVELOPMENT
Authors: Kristen Drucker, Thomas Kollmeyer, Connor Yanchus, Silvana De Lorenzo, Jeanette Eckel-Passow, Daniel Honore Lachance, Daniel Schramek, Robert Jenkins
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND The topologically associated domain (TAD) on 8q24 surrounding MYC is important for many types of cancer. The region is also important in the formation of IDH-mutant glioma; the risk allele rs55705857 being associated with the development of these tumors. The rs55705857 risk allele significantly increased the formation of tumors in an IDH-mutant mouse model. Cerebral organoids have been found to recapitulate the early development of the brain. We hypothesized that the rs55705857 risk allele may alter the phenotype of cerebral organoids. METHODS Isogenic induced pluripotent stem cells (iPSCs) were developed with (n=3) and without (n=2) the rs55705857 risk allele from the parental cell line PGP-1 (GM23338). These cells were cultured and differentiated into unpatterned cerebral organoids and observed throughout differentiation. Organoids were fixed, sectioned, and stained by H&amp;E and immunofluorescence. RESULTS Organoids containing the risk allele were smaller throughout development, starting at the embryoid body stage and continuing up to over 75 days in culture, compared to two isogenic non-risk lines. At 4 weeks the risk allele containing organoids also contained a larger number of small rosette-like neuroepithelia, instead of the more continuous neuroepithelia observed in the non-risk allele organoids. At 75 days, the organoids with the risk allele maintained a larger proportion of Sox2 positive cells, which are enriched in the tight clusters of small cells with round nuclei. CONCLUSIONS The risk allele rs55705857 in the MYC TAD at 8q24 is altering the development of unpatterned cerebral organoids. This difference is visible as early as embryoid body development and persists through neuroepithelial development. Further studies of these differences may help our understanding of how rs55705857 accelerates IDH-mutant glioma development.
MODL-08. ESTABLISHING IN VITRO MODELS TO RECAPITULATE PROTEIN-LEVEL PROGNOSTIC CELL PHENOTYPES FROM PRIMARY HUMAN GLIOBLASTOMA
Authors: Taylor McDonald, Silky Chotai, Todd Bartkowiak, Stephanie Medina, Madeline Hayes, Asa Brockman, Bret Mobley, Allen Sills, Peter Morone, Reid Thompson, Lola Chambless, Jonathan Irish, Rebecca Ihrie
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma (GBM) is a highly aggressive primary central nervous system tumor for which median survival continues to be low, despite multimodal treatment and surgical resection. Heterogeneity at many levels (genomic, cytoarchitectural, and metabolic) likely contributes to these poor outcomes, and single-cell approaches can help to identify prognostically meaningful cells and features within heterogeneous tumors at each of these levels. Recent studies using mass cytometry (CyTOF) and the accompanying analysis pipeline Risk Assessment Population Identification (RAPID) measured per-cell protein levels in &amp;gt; 2 million cells from 28 IDH1/2-wildtype primary glioblastoma tumors and identified 2 phenotypes within these tumors that are present in different abundances across patients and have contrasting prognostic value. Increased abundance of Glioblastoma Negative Prognostic (GNP) cells within these tumors is predictive of shorter overall survival (OS HR = 1.07 [95% CI 1.02–1.12], p = 0.003), while the converse is true for Glioblastoma Positive Prognostic (GPP) cells (OS HR = 0.93 [0.87–1.0], p = 0.05). To effectively study these phenotypes, reproducible in vitro models are needed that recapitulate the total protein expression and phosphorylation events that distinguish GNP and GPP cells. Using available RNA transcript data, a candidate subset of glioma stem cell models were identified and are now being profiled using standardized mass-tagged antibody panels. These culture models will be quantitatively compared against established GNP and GPP populations in patient tissue samples using the Marker Enrichment Modeling statistic as well as other machine learning tools. Development of these models will be critical to future experiments aimed at identifying possible mechanistic therapies that effectively eliminate each of these identified populations, as well as aligning these protein-level phenotypes to other genomic and functional data in glioblastoma samples and models.
MODL-15. BRINGING PRECISION MEDICINE TO GLIOBLASTOMA PATIENTS BY MODELING MOLECULAR TUMOR SUBTYPES IN IMMUNOCOMPETENT SWINE FOR THERAPEUTIC AND BIOMARKER DEVELOPMENT
Authors: Adrienne Watson, Derek Korpela, Nicholas Koes, Mandy Taisto, Stanislas Corbiere, Barbara Tschida
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma (GBM) is an aggressive primary brain tumor with no effective cure. Standard of care treatment offers dismal prognoses for patients with a median survival time of only 15.6 months, and no new drugs have been approved in 15 years. Contributing factors include tumor heterogeneity, high mutation rates, infiltrative growth, a complex tumor-immune microenvironment, and the blood-brain barrier, all of which are obstacles clinicians and researchers must overcome to improve patient outcomes. Research to identify novel therapeutic strategies are ongoing, but treatments that show promise in preclinical studies often do not pass Phase 2 and 3 clinical trials. These costly failures are attributable to a lack of predictive preclinical models that translate to human application, low patient availability for numerous and robust clinical trials, and an “all-comer” approach to clinical trial design where patients are enrolled based on disease presence and not molecular features of the tumor. To advance treatments for GBM, Recombinetics has pioneered somatic gene-editing technologies to the same genetic changes seen in patient tumors in GBM-initiating cells in an immune-competent swine model. These models rapidly and reproducibly develop GBM tumors that resemble human GBMs genetically, clinically and histologically. In addition to the physiological, immunological, and metabolic parallels between swine and humans, the molecular data collected from our swine mesenchymal and classical subtypes of GBM validate accurate disease modeling and we are pursuing additional GBM subtypes. Using RNA-sequencing, we are characterizing molecular profiles of these tumors, as well as identifying and validating drug targets. Studies are ongoing to characterize the tumor immune microenvironment of our models for improved immune-oncology therapeutic development. These large animal models of GBM will usher in a new era of pre-clinical testing that predicts the efficacy of a variety of therapeutic approaches, using precision medicine to bring novel, safe, and effective therapies to patients.